I've verified via ls -l /dev/disk/by-uuid that my drive where Ubuntu is installed matches the UUID that supposedly doesn't exist. The UUID of my thumb drive when inserted happens to be 06B3-9C68.

There is no mention of my USB drive's UUID anywhere in /boot/grub/grub.cfg

I've also tried to re-install GRUB after booting into my system, removing the stick, and running grub-install /dev/sda. It still happens, and I cannot boot without the USB drive inserted into the computer. And what really gets my goat is that the boot order of my system is CDROM>Hard Drive>USB. It's not even reaching the USB to try to boot from it, so why does it matter that it's not there?

Edit: Also, I ran grub-config without the stick in followed by another grub-install. Still no go.

Boot-Repair is a simple tool to repair frequent boot issues you may encounter in Ubuntu like when you can't boot Ubuntu after installing Windows or another Linux distribution, or when you can't boot Windows after installing Ubuntu, or when GRUB is not displayed anymore, some upgrade breaks GRUB, etc.

Another method that I've used to fix this type of situations, was by using Super Grub2 Disk to allow me to boot inside the Linux partition, and then use the administrative tools to fix my boot loader:

I don't get it though - If these are just tools to let you boot a system when the bootloader isn't working, why can't I just use grub-install again once I'm in by using the USB stick?
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agent154Jun 23 '12 at 18:16

Your problem seems to be the hd1 appearing in your grub.cfg. For a single disk system I'd expect that should be hd0. Assuming your UUIDs are correct, boot up with the stick, change the permissions on /boot/grub/grub.cfg to include w (sudo chmod +w grub.cfg), edit the file (sudo vi grub.cfg) and change every hd1 to hd0. save it, shutdown, remove the stick and reboot. At the grub menu, you may check the disks available -- enter c for the grub command line, then type "set root=" then tab for autocompletion. Multiple choices will be offered if available, but if only hd0 is available, it will be filled in to "set root=hd0," another tab will offer the partition choices, which should include the ones you want. Maybe the fix of editing the hd1 to hd0 would work directly from the grub menu, type e to edit, and change the hd1 s then F10 (or ctrl X)to reboot. If that works, fix things permanently with sudo update-grub.